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- EMDB-0232: Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosom... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0232 | |||||||||
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Title | Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the body of the small mitoribosomal subunit in complex with mt-IF-3 | |||||||||
![]() | map of the T. brucei mitoribosome small subunit body in complex with mt-IF3 | |||||||||
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Function / homology | ![]() modulation of formation of structure involved in a symbiotic process / organellar small ribosomal subunit / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / valine catabolic process / kinetoplast / quorum sensing / regulation of protein kinase A signaling ...modulation of formation of structure involved in a symbiotic process / organellar small ribosomal subunit / 3-hydroxyisobutyryl-CoA hydrolase / 3-hydroxyisobutyryl-CoA hydrolase activity / mitochondrial mRNA editing complex / mitochondrial RNA processing / valine catabolic process / kinetoplast / quorum sensing / regulation of protein kinase A signaling / enoyl-CoA hydratase activity / mRNA stabilization / ciliary plasm / mitochondrial small ribosomal subunit / superoxide dismutase / fatty acid beta-oxidation / protein kinase A regulatory subunit binding / superoxide dismutase activity / cytosolic small ribosomal subunit / hydrolase activity / ribosome / structural constituent of ribosome / translation / mitochondrion / RNA binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.27 Å | |||||||||
![]() | Ramrath DJF / Niemann M / Leibundgut M / Bieri P / Prange C / Horn EK / Leitner A / Boehringer D / Schneider A / Ban N | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Evolutionary shift toward protein-based architecture in trypanosomal mitochondrial ribosomes. Authors: David J F Ramrath / Moritz Niemann / Marc Leibundgut / Philipp Bieri / Céline Prange / Elke K Horn / Alexander Leitner / Daniel Boehringer / André Schneider / Nenad Ban / ![]() Abstract: Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , ...Ribosomal RNA (rRNA) plays key functional and architectural roles in ribosomes. Using electron microscopy, we determined the atomic structure of a highly divergent ribosome found in mitochondria of , a unicellular parasite that causes sleeping sickness in humans. The trypanosomal mitoribosome features the smallest rRNAs and contains more proteins than all known ribosomes. The structure shows how the proteins have taken over the role of architectural scaffold from the rRNA: They form an autonomous outer shell that surrounds the entire particle and stabilizes and positions the functionally important regions of the rRNA. Our results also reveal the "minimal" set of conserved rRNA and protein components shared by all ribosomes that help us define the most essential functional elements. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 11.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 61.4 KB 61.4 KB | Display Display | ![]() |
Images | ![]() | 50.8 KB | ||
Others | ![]() ![]() | 98.4 MB 98.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 393.3 KB | Display | ![]() |
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Full document | ![]() | 392.4 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hiyMC ![]() 0229C ![]() 0230C ![]() 0231C ![]() 0233C ![]() 6hivC ![]() 6hiwC ![]() 6hixC ![]() 6hizC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | map of the T. brucei mitoribosome small subunit body in complex with mt-IF3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: half map (even) of the T. brucei mitoribosome...
File | emd_0232_half_map_1.map | ||||||||||||
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Annotation | half map (even) of the T. brucei mitoribosome small subunit body in complex with mt-IF3 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map (odd) of the T. brucei mitoribosome...
File | emd_0232_half_map_2.map | ||||||||||||
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Annotation | half map (odd) of the T. brucei mitoribosome small subunit body in complex with mt-IF3 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : body of the T. brucei mitoribosome small subunit in complex with ...
+Supramolecule #1: body of the T. brucei mitoribosome small subunit in complex with ...
+Macromolecule #1: mS48
+Macromolecule #2: mS51
+Macromolecule #3: mS56
+Macromolecule #4: mS59
+Macromolecule #5: mS60
+Macromolecule #6: mS61
+Macromolecule #7: mS62
+Macromolecule #8: mS63
+Macromolecule #9: mS64
+Macromolecule #10: mS65
+Macromolecule #11: mS66
+Macromolecule #12: mS68
+Macromolecule #13: mS73
+Macromolecule #14: mS74
+Macromolecule #15: mS55m
+Macromolecule #16: bS6m
+Macromolecule #17: uS8m
+Macromolecule #18: uS9m
+Macromolecule #19: uS11m
+Macromolecule #20: uS12m
+Macromolecule #21: uS15m
+Macromolecule #22: bS16m
+Macromolecule #23: uS17m
+Macromolecule #24: bS18m
+Macromolecule #25: uS21m
+Macromolecule #26: mt-IF-3
+Macromolecule #27: mS22
+Macromolecule #28: mS23
+Macromolecule #29: mS26
+Macromolecule #30: mS34
+Macromolecule #31: mS37
+Macromolecule #32: mS38
+Macromolecule #33: mS41
+Macromolecule #34: mS42
+Macromolecule #35: mS43
+Macromolecule #36: mS47
+Macromolecule #38: Unknown protein
+Macromolecule #39: Unknown protein
+Macromolecule #40: Unknown protein
+Macromolecule #41: Unknown protein
+Macromolecule #37: 9S rRNA
+Macromolecule #42: ZINC ION
+Macromolecule #43: MAGNESIUM ION
+Macromolecule #44: SPERMIDINE
+Macromolecule #45: SPERMINE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 98 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | We used Coot and O for initial model building and refined the structure using Phenix |
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Refinement | Protocol: AB INITIO MODEL / Overall B value: 41.4 |
Output model | ![]() PDB-6hiy: |